mod_gsea {CEMiTool} | R Documentation

## Module Gene Set Enrichment Analysis

### Description

Perfoms Gene Set Enrichment Analysis (GSEA) for each co-expression module found.

### Usage

    mod_gsea(cem, ...)

    ## S4 method for signature 'CEMiTool'
    mod_gsea(
      cem,
      gsea_scale = TRUE,
      rank_method = "mean",
      gsea_min_size = 15,
      gsea_max_size = 1000,
      verbose = FALSE
    )

### Arguments

`cem` | Object of class `CEMiTool`.
`...` | Optional parameters.
`gsea_scale` | If TRUE, transform data using z-score transformation. Default: TRUE
`rank_method` | Character string indicating how to rank genes. Either "mean" (the default) or "median".
`gsea_min_size` | Minimum gene set size (Default: 15).
`gsea_max_size` | Maximum gene set size (Default: 1000).
`verbose` | logical. Report analysis steps.

### Value

GSEA results.

### See Also

`plot_gsea`

### Examples

    # Get example CEMiTool object
    data(cem)
    # Look at example annotation file
    sample_annotation(cem)
    # Run GSEA on network modules
    cem <- mod_gsea(cem)
    # Check results
    gsea_data(cem)

[Package CEMiTool version 1.14.1 Index]